HIV gp41 is a heavily glycosylated transmembrane protein. The difficulty in producing full length recombinant gp41 necessitates an incremental approach for structural determination studies. The ectodomain region, located on the outer surface of the viral membrane directly mediates membrane fusion events via an N-terminal fusion domain (FD). In our previous work both the NMR and X-ray structures of a truncated gp41 ectodomain (lacking FD) were determined. The structures indicated a rod-like trimer comprising three parallel N-terminal alpha-helices assembled as a coiled-coil in the center with three antiparallel C-terminal alpha-helices packed on the outside with highly flexible loops connecting the inner and outer helices (6-helical bundle: 6HB). We have also described the structure of the FD which consists of an N-terminal helix with a C-terminal linker region. To understand in more detail the interaction between the fusion domain and the membrane anchor, constructs were made which included the N-terminal FD- 6 HB - linker region - transmembrane region. This complex membrane protein (gp41-190) which contains two membrane associating regions (FD and transmembrane domain) was expressed in bacteria and purified as a protein-detergent complex. Considerable effort has been made to determine those detergents most suited for maintaining the solubility of the protein and at the same time being compatible with structural studies, especially by NMR. Using analytical ultracentrifugation and other biophysical methods, the protein complex was shown to be physical homogenous and have a homotrimeric subunit structure (similar to the water soluble ectodomain alone). High resolution NMR techniques are being used to determine the structure and conformational flexibility of the gp41-190. This is a major undertaking given the high molecular weight of the protein - complex (close to 100,000). The FD domain is highly mobile and not associated in the same detergent micelles (equivalent to lipid bilayer) as the transmembrane region. The structural determination of protein by NMR will allow rapid mapping of the interaction sites of drug and antibodies. With the current improvements made in the protein preparations, we are also reexamining condition for protein crystallization. These structural studies will provide insight into the fusion mechanism and so provide direction for targeted anti-HIV intervention.